Get predicted PPI

Description

Get the predicted PPI of an Path2PPI object consisting of each predicted interaction and protein in the target species.

Usage

getPPI(path2ppi, raw=FALSE, igraph=FALSE)

Arguments

Value

See igraph argument.

Author(s)

Oliver Philipp MolBI-software@bioinformatik.uni-frankfurt.de

See Also

getHybridNetwork

Examples

data(ai) #Load test data set

ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")

ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins, 
                    human.ai.irefindex, pa2human.ai.homologs)
ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", 
                    yeast.ai.proteins, yeast.ai.irefindex, 
                    pa2yeast.ai.homologs)

ppi <- predictPPI(ppi)

#Get the predicted PPI as data frame.
network <- getPPI(ppi)

#Get the detailed predicted PPI as data frame.
network.raw <- getPPI(ppi,raw=TRUE)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Path2PPI)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Path2PPI/getPPI.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getPPI
> ### Title: Get predicted PPI
> ### Aliases: getPPI
> 
> ### ** Examples
> 
> data(ai) #Load test data set
> 
> ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145")
> 
> ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins, 
+                     human.ai.irefindex, pa2human.ai.homologs)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", 
+                     yeast.ai.proteins, yeast.ai.irefindex, 
+                     pa2yeast.ai.homologs)
Search for all relevant interactions:
0%--25%--50%--75%--100%
Remove irrelevant homologs.
> 
> ppi <- predictPPI(ppi)
Begin with Homo sapiens
6 interactions processed. These lead to 0 interactions in target species.
-------------------------------
Begin with Saccharomyces cerevisiae (S288c)
15 interactions processed. These lead to 8 interactions in target species.
-------------------------------
Combine results to one single PPI.
A total of 8 putative interactions were predicted in target species.
> 
> #Get the predicted PPI as data frame.
> network <- getPPI(ppi)
> 
> #Get the detailed predicted PPI as data frame.
> network.raw <- getPPI(ppi,raw=TRUE)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>